2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.dbsources;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.DBRefSource;
26 import com.stevesoft.pat.Regex;
29 * Test class for accessing GeneDB - not yet finished.
34 public class GeneDbSource extends EmblXmlSource
45 * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
48 public String getAccessionSeparator()
50 // TODO Auto-generated method stub
57 * @see jalview.ws.DbSourceProxy#getAccessionValidator()
60 public Regex getAccessionValidator()
62 // TODO Auto-generated method stub
69 * @see jalview.ws.DbSourceProxy#getDbSource()
72 public String getDbSource()
74 return DBRefSource.GENEDB;
80 * @see jalview.ws.DbSourceProxy#getDbVersion()
83 public String getDbVersion()
85 // TODO Auto-generated method stub
92 * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
95 public AlignmentI getSequenceRecords(String queries) throws Exception
98 // http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL
100 return getEmblSequenceRecords(DBRefSource.GENEDB, queries);
106 * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
109 public boolean isValidReference(String accession)
111 // TODO Auto-generated method stub
116 * return T.Brucei Mannosyl-Transferase TbPIG-M
119 public String getTestQuery()
121 return "Tb927.6.3300";
125 public String getDbName()
127 return "GeneDB"; // getDbSource();